DNA-micro/nanoparticle motors are burnt-bridge Brownian ratchets moving on an RNA-modified surface driven by Ribonuclease H (RNase H), and are one of the fastest artificial molecular motors. Interestingly, these motors show a maximum speed of ∼30 nm s −1 irrespective of the particle size ranging from 100 to 5,000 nm, whereas the run-length increases with the particle size (K. Yehl. et al. 2016. Nat. Nanotechnol. 11, 184; T. Harashima. et al. 2025. Nat. Commun. 16, 729). Here, we performed geometry-based kinetic simulations of DNA-micro/nanoparticle motors with the sizes of 100, 500, 1,000, and 5,000 nm to identify the factors governing speed, run-length, and unidirectionality. The simulations reproduced the experiments quantitatively, and the speed remained constant for the motors with different particle sizes. The constant speed was caused by a trade-off between the pause length and the step size, both of which increased with the particle size. In contrast, the run-length and the unidirectionality increased with the particle size because large particles had higher multivalency suppressing stochastic detachment and increased RNA hydrolysis efficiency under the motor trajectory. For the smallest 100-nm particle, the run-length was improved from 0.6 to 2 μm by increasing the DNA/RNA hybridization rate from 0.2 to 0.8 s −1 . Furthermore, the speed increased to 200 nm s −1 by 10-fold increases in DNA/RNA hybridization, RNase H binding, and RNA hydrolysis rates (8.0 and 72, 30 s −1 , respectively). In addition, if we consider the rotational diffusion of the particle, the speed for the largest 5000 nm particle was limited to 100 nm s −1 , because the time required for rolling motion (∼0.3 s) became comparable to the pause length. Our results indicate that DNA-particle motors must possess a nanoscale body to achieve a speed exceeding 100 nm s −1 .
Harashima et al. (Sun,) studied this question.
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